Alignment of deduced amino acid sequences of the pol gene of human endogenous C-type proviral DNA and corresponding sequences from a variety of retroviruses forund in man (HTLV-I, -II, -III), ape, cow, sheep, mouse and chicken shows little homology in the region encoding reverse transcriptase even though the enzyme performs the same function in all retroviruses. A highly conserved small domain was identified in reverse transcriptases as well as in transposons and other sequences attributed to having reverse transcriptase function. Moloney murine leukemia virus (Mo-MuLV) is being used as a model system to evaluate the significance of these conserved sequences. Site specific mutagenesis has been used to change the codons of the conserved amino acids. The normal sequence has been replaced in MoMuLV and in a reverse transcriptase-containing expression vector to permit evaluation of these mutations biologically in infected cells and biochemically in an in vitro system, respectively. Of the four C-type murine retroviruses known, three (ecotropic, xenotropic and MCF MuLVs) can exist as integrated sequences in mouse genomic DNA; definitive results had not been obtained for the fourth type, amphotropic MuLV. It has not been possible to determine number of copies or types of each of the MuLVs or to follow the genesis of MCF MuLV (which is associated with leukemia in mice) since a specific hybridization probe was available only for ecotropic MuLVs. We have developed individual probes for MCF, xenotropic and amphotropic MuLVs which hybridize specifically with the env region of the respective MuLV. Analysis of genomic DNA of inbred laboratory mice show all mice have many copies of MCF and xenotropic sequences with more copies of the former. Wild mice, on the other hand, may have neither sequence of both sequences. These data indicate mouse speciation occurred before MCF or xenotropic MuLVs were integrated into the germline. No mice have amphotropic sequences suggesting they represent an exogenous rather than an endogenous type virus.